RETROELEMENTS IN THE LOW-COPY KINETIC COMPONENT OF THE Pinus taeda GENOME

Texas A&M University, Genetics and Forest Science, College Station, TX 77843-2135 USA

Retrotransposons such as the highly repetitive IFG and TPE1 elements have played a major role in gymnosperm genome size amplification. However, highly repetitive elements are reported to account for only 11 to 18 % of the genome. Increased DNA content of pine compared to angiosperm genomes is apparent in all of the pine DNA kinetic classes, not just highly repetitive DNA. The pine low-copy kinetic component is larger than many entire angiosperm genomes. Pinus taeda low-copy DNA was sampled to test the hypothesis that the large low-repetitive and single-copy kinetic components contain retrotransposons. Twenty-five percent of the fragments matched LINE-, gypsy- or copia-like retrotransposons. Retroelement copy numbers ranged from one to 400. Protein sequence alignments indicated that these elements are diverse. Most appeared to be nonfunctional, and may have diverged from functional elements that originated in the low-, middle- or highly-repetitive components. Isolation of retroelements from the low-copy kinetic component suggested that they are a major source of excess low-copy DNA. The P. strobus C₀T curve was reanalyzed to test the hypothesis that the large pine low-copy kinetic component was a function of C₀T curve analysis. Reanalysis using the new P. strobus genome size estimate indicated that the single-copy component was 14 %, or approximately 3900 Mb, of the P. strobus genome. The single-copy component was smaller than the 24 % previously estimated, but still in excess compared to angiosperm genomes. Both C₀T analysis and retroelements were factors contributing to the excess low-copy DNA in pine compared to angiosperms.